App syncing

I am noticing that iTunes does not want to sync my apps and folders.

It seems to want to sync some random arrangement that is not what I have created on my iPhone.

iPhone Apps
Not sure if this is what you are experiencing, but here is what I have noticed on my both my iPad and iPhone when syncing apps:

The scenario is:
(1) I delete some of the apps from the APPS list in iTunes using the 'delete key' on my keyboard and I select option to 'leave the files' instead of 'remove to trash'.

(2) The apps that I deleted do not show up as an option in my 'apps tab' when connecting a device. I sync and those apps are removed from the device, which is what I wanted.

(3) However, when I check for updates and update all via the option at the bottom of the iTunes Apps Window in iTunes, these 'deleted' apps (which I assume must still be on my purchase list with Apple) get added back into the Apps list as 'new apps' and I assume are then recognized as 'new apps'.

(4) Since I have 'Sync new apps' option checked, they get put back onto my devices with the subsequent sync. This is evident on my iPhone as they appear as icons that are not in any folder. On my iPad since all the pages are full, they appear when I use a spotlight search and are clickable from the search list and can be run.

There seems to still be some problems with app syncing as far as I can tell.

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I realize I didn't really give enough details.

I had synced previously without issue. Then when I noticed the sync apps box was not checked, I checked it, and it warned me that it would overwrite the apps on the iphone, which seemed odd.

Also, the view (in iTunes) of the apps as they are on the iphone changed to some random arrangement without any of the folders I have and with different apps selected.

This is very similar to one of the posts I saw on the apple discussions page. I did not perform the sync with the apps.